MolNFT v1 · #182918 · protein

Pptt PAP(COA) 8978B complex

7N8M · 4'-phosphopantetheinyl transferase pptt: “Pptt PAP(COA) 8978B complex”. X-ray diffraction, 3 ligands (17I, COA, MG), 3 pockets (best druggability 0.71). MolNFT v1 #182918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7N8M
Type: protein
Length: 442 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4'-phosphopantetheinyl transferase pptt
EC: 2.7.8.7
UniProt: O33336
Ligands: 17I, COA, MG
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	4'-phosphopantetheinyl transferase pptt (EC 2.7.8.7)	protein	221	30% helix, 29% strand	O33336

Ligands and binding sites

17I · N-(2,6-diethylphenyl)-N'-(N-methylcarbamimidoyl)urea · ligand · 3 copies · chains A, B
COA · Coenzyme A · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 7 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	506	0.71	0.80	61	COA, 17I, MG, GOL
2	399	0.68	0.80	48	COA, 17I, MG
3	102	0.36	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 338 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7N8M · PptT PAP(CoA) 8978B complex · the same entry in another collection · chain A against A, TM-score 1.00
O33336 · AlphaFold monomer V2.0 prediction for 4'-phosphopantetheinyl transferase pptt (O33336) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O33336
Elsewhere: RCSB PDB 7N8M · PDBe 7N8M · UniProt O33336

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